Nextflow for reproducible and automated data analysis
Nextflow for reproducible and automated data analysis
7 December 2026, 9h30- 17h00
8 December 2026, 9h30-17h00
General context
This hands-on course introduces the principles and practice of building scalable and reproducible data analysis pipelines using Nextflow. As bioinformatics data volumes increase and analyses become more complex, workflow management tools play a key role in ensuring reproducibility and efficiency.
During the training, you will learn to develop and run pipelines on local machines, HPC clusters, and cloud platforms. Starting with the basics, the course guides you through creating a simple pipeline and enhancing it with Nextflow’s modern DSL2 syntax.
- Describe the core components of Nextflow (e.g., channels, processes, modules, workflows)
- Explain the roles of each component in pipeline development and the reproducibility aspect
- Construct a basic Nextflow pipeline using DSL2 syntax and execute it on a local machine.
- Modify configuration files to adapt pipeline parameters for different computing environments (e.g., local, cluster, cloud).
- Apply best practices for reproducibility and scalability in workflow design.
- Debug and refactor a simple pipeline to improve clarity, modularity, and performance.
The training combines theoretical sessions with hands-on activities. In the end, a small challenge invites you to apply all the skills you have learned.
Check this opportunity: Reproducible Data Analysis: an essential capability in modern science.
Researchers with no or little knowledge of containers or workflow pipelines.
- Completion of an HPC course is mandatory for individuals without prior experience in High Performance Computing before enrolling.
- You're familiar with doing bioinformatics on the command line and with Docker containers.
- If you have no experience with the command line, we strongly recommend following the Linux initiation training first or the self-paced e-learning.
- If you have no experience with Docker, you can follow our training "Containerise data analysis with Docker & Apptainer".
This course is part of the learning path Reproducible data analysis.
Trainers
Kobe Lavaerts
Bioinformatician at VIB Nucleomics Core in Leuven. Currently mainly focusing on operating and developing routine pipelines for processing raw sequencing data.
Maria Tsontaki
Maria Tsontaki is a Project Manager at the VIB Data Core. Previously working as a Bioinformatics Scientist in biotech, she is now part of the Data Core Compute team, ensuring researchers have access to computational resources and advanced software tools for scalable, reproducible data analysis. Her tasks in the team range from identifying and coordinating user needs and requests to providing bioinformatics-related support.
Nicolas Vannieuwkerke
Nicolas Vannieuwkerke is a bioinformatician at CMGG (UZ Ghent) who mainly focuses on developing and maintaining Nextflow pipelines for the diagnostic NGS analyses. He is a very active member of the Nextflow community as a Nextflow ambassador and is part of the nf-core core team. Nf-core is the largest Nextflow community that creates and maintains a number of best-practice pipelines and developer resources.
Program
Building Blocks
Coffee break (provided)
Processes and Workflows
Lunch (provided)
Creating our first pipeline
Coffee break (provided)
Modules and Subworkflow
Config files, Containers and Reports
Coffee break (provided)
Exercise
Lunch (provided)
Project Challenge
Coffee break (provided)
Project Challenge
Practical info
07 December 2026 - 08 December 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
07 December 2026 - 08 December 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
07 December 2026 - 08 December 2026
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
07 December 2026 - 08 December 2026
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.